Cotton (Gossypium spp.) is an important fiber and oil seed crop throughout the world. In most other cotton-producing countries, including the United States, cotton is grown as an annual crop, although its natural growth habit is perennial in nature. The genus Gossypium comprises approximately 50 known species, which are native to and and semi-arid regions of the Americas, Asia, Africa and Australia. Fryxell (1992) Rheedea 2:108-65. These species populate several genomic groups based on chromosome size and homologous chromosome pairing in inter-specific hybrids, including eight groups of diploid plants and 1 group of tetraploid plants (i.e., “AD” genome). The majority of cotton fiber is produced by G. hirsutum (“Upland cotton”), which is a species of the tetraploid AD genome group. Furthermore, while cotton cultivation is largely dependent on these high-yielding Upland cotton cultivars, they are low in genetic variation relative to other plant taxa, and are considered to be vulnerable to pathogen and insect infection. Brubaker & Wendel (1994) Am. J. Bot. 81:1309-26; Bowman et al. (1996) Crop Sci. 36:577-81.
In recent years, the yields of cotton in many parts of USA and other nations has been affected by infection with the parasite, reniform nematode (“RN”) (Rotylenchulus reniformis). Reniform nematode parasitism in cotton involves the formation of syncytia to provide nutrition for the developing female, and the events that occur at this feeding site may determine the degree of susceptibility of cotton plants to the nematode. Agudelo et al. (2005) J. Nematology 37:185-9; Rebois et al. (1975) J. Nematology 7:122-39.
There are few tools available to combat RN crop damage. For example, nematicides such as TEMIK® and soil fumigants such as TELONE® have been used to reduce the detrimental effect of reniform nematodes on the yield of cotton, but these nematicides are only partially effective when they are used as indicated. Host plant resistance would be the most economically feasible means to manage reniform nematode infestations, but no Upland cotton cultivar is resistant to RN. Robinson et al. (1999) Crop Sci. 39:850-8; Koenning et al. (2004) Plant Dis. 88:100-13; Usery et al. (2005) Nematropica 35:121-33; Weaver et al. (2007) Crop Sci. 47:19-24.
Reniform nematode resistance has been identified in wild diploid species, such as G. longicalyx (Dighe et al. (2009) Crop Sci. 49:1151-64) and G. aridium (Romano et al. (2009), supra) as well as an allotetraploid genotype: Inca Cotton GB713 (Gutiérrez et al. (2011) TAG Theor. Appl. Genet. 122:271-80). A single dominant gene has been identified as responsible for the inheritance of RN resistance obtained from the introgression of G. longicalyx into G. hirsutum. Robinson et al. (2007) Crop Sci. 47:1865-77. In addition, dominant genes at two different loci have been identified as responsible for the inheritance of resistance to RN obtained from the introgression of G. arboreum and G. aridum (Rose & Standley) Skovsted. Sacks & Robinson (2009) Field Crops Res. 112:1-6. It is important to identify as many useful sources of RN resistance as possible. Multiple resistance sources may prove an invaluable resource if and when resistance-breaking nematode populations or races are encountered or develop.
The introgression of traits (e.g., RN resistance) from other sources into Upland cotton is a lengthy and challenging process, because for example, cotton genetics is complicated, involving differences in ploidy and the existence of various genomes and sub-genomes, many of which are incompatible or have low compatibility. Robinson (2007), Annu. Rev. Phytopathol. 45:263-88; Percival et al. (1999), “Taxonomy and germplasm resources,” In Cotton: Origin, History, Technology, and Production. Smith & Cothren (eds.), New York, N.Y., John Wiley & Sons, pp. 33-63. Moreover, the survival of plants resulting from inter-specific crosses is low due to chromosome pairing difficulties, and there is an even lower probability of obtaining agronomically suitable progeny with the desired introgressed genetic material. See Romano et al. (2009) TAG Theor. Appl. Genet. 120:139-50. Where it has been possible, traits of interest have been introgressed into Upland cotton from diploid species via hexaploid bridging lines. See, e.g., Robinson et al. (2007), supra; Konan et al. (2007) Plt. Breed 126:176-81.
Plant breeding programs combine desirable traits from two or more cultivars or various broad-based sources into breeding pools, from which cultivars are developed by selfing and selection of desired phenotypes. The goal is to combine in a single variety an improved combination of desirable traits from the parental germplasm. There are numerous steps in such a program for the development of a new cultivar comprising one or more desired trait(s). Plant breeding begins with the analysis and definition of problems and weaknesses of the current germplasm, the establishment of program goals, and the definition of specific breeding objectives. Germplasm that possess the traits to meet the program goals must be selected, where any two germplasms may be incompatible or poorly compatible, particularly in the case of a plant such as cotton, which has complicated genetics.
Each breeding program should include a periodic, objective evaluation of the efficiency of the breeding procedure. Evaluation criteria vary depending on the goal and objectives, but should include gain from selection per year (based on comparisons to an appropriate standard), overall value of the advanced breeding lines, and the number of successful cultivars produced per unit of input (e.g., per year, per dollar expended, etc.). Promising advanced breeding lines are then thoroughly tested and compared to appropriate standards in environments representative of the commercial target area(s) for three or more years. Candidates for new commercial cultivars are selected from among the best lines; those still deficient in a few traits may be used as parents to produce new populations for further selection. These processes, which lead to the final step of marketing and distribution, usually take from 8 to 12 years from the time the first cross is made. Therefore, development of new cultivars is a time-consuming process that requires precise forward planning, efficient use of resources, and a minimum of changes in direction.
A most difficult task in plant breeding is the identification of individuals that are genetically superior. One method of identifying a superior plant is to observe its performance relative to other experimental plants and to a widely grown standard cultivar. If a single observation is inconclusive, replicated observations may be used to provide a better estimate of its genetic worth. This task is extremely difficult, because (for most traits) the true genotypic value is masked by other confounding plant traits or environmental factors.
The practitioner's choice of breeding and selection methods depends on the mode of plant reproduction, the heritability of the trait(s) being improved, the type of cultivar used commercially (e.g., F1 hybrid cultivar, pureline cultivar, etc.), and the complexity of the trait's inheritance. For highly heritable traits, a choice of superior individual plants evaluated at a single location may be effective, whereas for traits with low heritability, selection should be based on mean values obtained from replicated evaluations of families of related plants. Popular selection methods commonly include pedigree selection, modified pedigree selection, mass selection, and recurrent selection. Backcross breeding may be used to transfer one or a few favorable genes for a highly heritable trait into a desirable cultivar. Various recurrent selection techniques may be used to improve quantitatively-inherited traits controlled by numerous genes.
The breeder initially selects and crosses two or more parental lines, followed by repeated selfing and selection, producing many new genetic combinations. The breeder can theoretically generate billions of different genetic combinations via crossing, selfing, and mutagenesis. Such a breeder has no direct control of the process at the cellular level. Therefore, two breeders will never develop the same line, or even very similar lines, having the same traits.
Each year, the plant breeder selects the germplasm to advance to the next generation. This germplasm is grown under unique and different geographical, climatic, and soil conditions. Further selections are then made, during and at the end of the growing season. The cultivars that are developed are unpredictable. This unpredictability is due to the breeder's selection, which occurs in unique environments, and which allows no control at the DNA level (using conventional breeding procedures), with millions of different possible genetic combinations being generated. A breeder of ordinary skill in the art cannot predict the final resulting lines he develops, except possibly in a very gross and general fashion. Similarly, the same breeder cannot produce the same cultivar twice by using the exact same original parents and the same selection techniques. In the process of developing superior new cotton cultivars, this unpredictability results in the expenditure of large amounts of resources, monetary and otherwise.
Marker-assisted selection (MAS) may be used when it is available to provide significant advantages with respect to time, cost, and labor, when compared to phenotyping in the selection of progeny plants. Single nucleotide polymorphism (SNP) markers have become the markers of choice for MAS in several crop improvement programs, because of their higher abundance, amenability for automation, and availability of high throughput genotyping platforms. However, in cultivated cotton species, the high genomic complexity, narrow genetic base, allotetraploid nature, and lack of a reference genome hinder the development of candidate SNP markers.